Despite many improvements in the quality and reliability
of Josephson
junctions, the understanding of their noise sources, particularly
the effect of oxidation parameters on the atomic arrangement of the
interface and barrier layers, remains elusive. Here, we apply a Voronoi
tessellation, a geometrically structural and topological analysis,
to the amorphous barriers in aluminum oxide junctions. To enable this
analysis, we perform million-atom molecular dynamics simulations to
develop oxidation models at different temperatures. We find that the
temperature introduces noise by changing the atomic compactness of
oxides in the junctions. High-temperature oxidation aggravates the
structural disorder and surface roughness of the barrier. This work
will pave the way for illustrating the microscopic noise origin of
amorphous oxides, which can transform our fundamental understanding
of noncrystalline materials and qubit decoherence mechanisms.